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At least 361 records · Page 20

Effects of sampling techniques on short-term survival and genotyping success of salmonid fry

ABSTRACT Objective Genetics tools have become an integral part of managing and understanding fish populations. Generally, a small tissue sample, such as a fin clip, is taken and then genotyped, with little effect on survival of the fish. However, tissue sampling may have a larger effect on juvenile fish survival compared to their adult counterparts. We evaluated survival and genotyping success of various genetic sampling techniques for Chinook Salmon Oncorhynchus tshawytscha and Rainbow Trout Oncorhynchus mykiss fry. Methods Three sampling treatments were evaluated including control (anesthetized and handled), fin clipping (partial caudal fin clip), and swabbing (OmniSwab was used to collect external mucus). Survival was monitored for 12 d posttreatment, and genotyping success was evaluated. Results Survival was high in all treatment groups (i.e., 0.93–1.00) but, on average, was lower in the swab treatment group. Genotyping was successful in 100% of the fin clip samples and 11–50% of the swab samples. Conclusions Results of this study suggest that sampling caudal-fin tissue does not negatively affect fry short-term survival and the small tissue samples yield highly successful genotyping results. Swabbing did not produce successful genotyping results, and fish sampled with swabs experienced higher mortality than those that received fin clips. Results indicate that fin clips should be used for collection of genetic samples from fry.

McCarrick, Darcy K.↗

Small Particle Glovebox Experiments - Preliminary Results

A substantial portion of the asteroid samples returned by the HAYABUSA2 and OSIRIS-REx missions will consist of small (submm) components (due to the collection of those particles on the asteroid surface and due to the fragmenting of larger, friable material post-collection). In order to minimize the alteration/oxidation of asteroid regolith, the bulk collections will be stored and curated in nitrogen purged gloveboxes. The processing of small particles in an N2 glovebox will present challenges that are different from those experienced during lunar and meteorite sample processing. Particles in this size range are susceptible to unpredictable electrostatic charging that can result in sample loss during processing operations. Methods for the handling of sub-mm particles have been well developed for environments with ambient atmospheric conditions and relative humidity (RH) ranges between 40-70%. In such conditions, a number of factors can be successfully employed to minimize the effects of triboelectric charging, including the use of Po-210 sources that neutralize excess charge and the utilization of conductive manipulation tools and sample substrates. However, relative humidity levels above 40% also contribute significantly to dissipation of triboelectric effects. We had not previously investigated our charge mitigation methods in a completely dry, nitrogen-purged environment, or whether they would be sufficient in enabling the successful processing of sub-mm samples. Current glovebox configurations in use in our lunar and meteorite curation laboratories are optimized for the processing of macroscopic samples and tools; these glovebox designs are likely unsuitable for the processing of collections for which the bulk collection is comprised of sub-mm components. Small particle sample preparation requires the use of an optical magnification instrument – typically a stereo binocular microscope with at least 20x magnification. Current glovebox designs are not optimized for the utilization or integration of stereo microscopes; while many current cabinets include microscope viewports that enable the use of small, externally mounted stereo microscopes, the focusing methods (usually involving the use of a lab jack) lack the fidelity and precision required for small particle manipulation and imaging. Working distances of higher (>50x magnification) objective lenses may preclude the external use of a stereo microscope through a viewport; in order to successfully manipulate and image very small (< 20m) particles, stereo and digital microscope systems that are integrated within the glovebox should be investigated. Finally, ergonomic considerations for small particle work within a glovebox must be considered to minimize risk of injury to sample processors. In order to investigate some of the unknown parameters relating to small particle processing within an N2 glovebox, we conducted preliminary, qualitative experiments utilizing a small lunar cabinet that was originally used for film development.

C. J. Snead↗

JGI-Trichoderma v1.0

There is a series of Python and bash scripts to parse genomics datasets used to evaluate the coevolution of gene families and the feature importance of gene families using an SVM classifier. - Cover analysis: takes a list of single-copy genes in a set of genomes, aligns and builds the gene trees to determine if two gene families have a signature of covariation with one another. It parses the files to run phykit cover script described here: https://jlsteenwyk.com/PhyKIT/usage/index.html - SVM-classifier: This Python script is an SVM-based genomic classifier designed for biological data analysis. It combines machine learning with feature selection to identify important genomic markers and classify biological samples. Core Functionality: The script uses Support Vector Machines from scikit-learn to classify genomic data, incorporating SelectKBest for automated feature selection and leave-one-out cross-validation for performance assessment. It operates in multiple modes: feature ranking, optimal combination discovery, and sample prediction. Primary Applications: Genomic sample classification and biomarker discovery Feature importance analysis in high-dimensional biological datasets Prediction of sample categories based on genomic profiles Research applications requiring robust classification of biological data Key Advantages: High-dimensional handling: SVMs excel with genomic data's typical high feature-to-sample ratios Integrated feature selection: Reduces noise and computational overhead while identifying key markers Probability estimation: Provides confidence scores essential for biological interpretation Validation robustness: Leave-one-out cross-validation ensures reliable performance metrics Operational flexibility: Multiple analysis modes support different research phases from exploration to prediction

Stecca Steindorff, Andrei [Lawrence Berkeley Natio↗

PISCES two-detector covariance matrix fit for the NOvA Experiment

NOvA is a long-baseline neutrino oscillation experiment with two functionally identical detectors: a Near Detector (ND) at Fermilab, placed 1 km from the neutrino source, and a Far Detector (FD) located 810 km away from the ND in Minnesota. NOvA's primary physics goals are the precise measurements of neutrino oscillation parameters $\theta_{23}$ and $\Delta m^2_{32}$ , determine the neutrino mass ordering, and constrain the value of $\delta_{CP}$, via the study of muon neutrino to electron neutrino oscillation. In the standard NOvA three-flavor analysis, oscillation parameters are extracted using an extrapolation technique in which the ND data constrain the FD prediction through a ratio method. While this allows for systematic uncertainties sharing the same effects in both detectors to cancel, it remains an FD-only fit and does not fully leverage the constraining power of the high-statistics ND. This analysis proposes a simultaneous ND+FD fit using the PISCES method. PISCES (Parameter Inference with Systematic Covariance and Exact Statistics) is a framework designed to support complex configurations such as a joint ND+FD fit. This allows PISCES to take full advantage of the ND data to directly constrain systematic uncertainties across all samples. In PISCES, systematic uncertainties are encoded in a fractional covariance matrix, and statistical uncertainties are handled with a Poisson likelihood, making the approach well suited for low-statistics samples. For interpretability, we further use a Newton–Raphson + PCA method to recover per-systematic pulls from the covariance formulation. This poster presents the full PISCES joint ND+FD fit for the NOvA three-flavor analysis, describes its implementation and evaluates its performance through extensive robustness tests and fake data studies. It also provides a comparison between the PISCES joint ND+FD results and the standard NOvA extrapolation method.

Rajaoalisoa, Miriama [Cincinnati U.] (ORCID:000000↗

Ceramics for Molten Materials Containment, Transfer and Handling on the Lunar Surface

As part of a project on Molten Materials Transfer and Handling on the Lunar Surface, molten materials containment samples of various ceramics were tested to determine their performance in contact with a melt of lunar regolith simulant. The test temperature was 1600 C with contact times ranging from 0 to 12 hours. Regolith simulant was pressed into cylinders with the approximate dimensions of 1.25 dia x 1.25cm height and then melted on ceramic substrates. The regolith-ceramic interface was examined after processing to determine the melt/ceramic interaction. It was found that the molten regolith wetted all oxide ceramics tested extremely well which resulted in chemical reaction between the materials in each case. Alumina substrates were identified which withstood contact at the operating temperature of a molten regolith electrolysis cell (1600 C) for eight hours with little interaction or deformation. This represents an improvement over alumina grades currently in use and will provide a lifetime adequate for electrolysis experiments lasting 24 hours or more. Two types of non-oxide ceramics were also tested. It was found that they interacted to a limited degree with the melt resulting in little corrosion. These ceramics, Sic and BN, were not wetted as well as the oxides by the melt, and so remain possible materials for molten regolith handling. Tests wing longer holding periods and larger volumes of regolith are necessary to determine the ultimate performance of the tested ceramics.

Standish, Evan↗

Material handling device Patent

Device which separates and screens particles of soil samples for vidicon viewing in vacuum and reduced gravity environments

Ritchie, D. G.↗

Rescue and Preservation of Sample Data from the Apollo Missions to the Moon

Six Apollo missions landed on the Moon from 1969-72, returning to Earth 382 kg of lunar rock, soil, and core samples. These samples are among the best documented and preserved samples on Earth that have supported a robust research program for 45 years. From mission planning through sample collection, preliminary examination, and subsequent research, strict protocols and procedures are followed for handling and allocating Apollo subsamples, resulting in the production of vast amounts of documentation. Even today, hundreds of samples are allocated for research each year, building on the science foundation laid down by the early Apollo sample studies and combining new data from today's instrumentation, lunar remote sensing missions and lunar meteorites. Much sample information is available to researchers at curator.jsc.nasa.gov. Decades of analyses on lunar samples are published in LPSC proceedings volumes and other peer-reviewed journals, and tabulated in lunar sample compendia entries. However, for much of the 1969-1995 period, the processing documentation, individual and consortia analyses, and unpublished results exist only in analog forms or primitive digital formats that are either inaccessible or at risk of being lost forever because critical data from early investigators remain unpublished.

Todd, Nancy S.↗

f-Element complexes with benzyl and cyclohexyl substituted trihydroborates

Actinide complexes containing the simplest borohydrides (BH 4 ) 1- and (MeBH 3 ) 1- can exhibit remarkably highly volatility, which creates unique hazards and handling challenges, especially when making measurements on solid samples under vacuum. Here we describe efforts to prepare new actinide borohydride complexes with attenuated volatility by adding bulkier benzyl (Bn) and cyclohexyl (Cy) substituents to boron. Reactions of ThCl 4 , UI 3 (thf) 4 , and NdI 3 with the mixed alkali metal salt Li/K(BnBH 3 )(thf) n yielded Th(BnBH 3 ) 4 (thf) 2 , U(BnBH 3 ) 4 (thf) 2 , and K[Nd(BnBH 3 ) 4 ], respectively. Notable amongst these, the reaction with UI 3 (thf) 4 proceeds via oxidation of U(III) to U(IV) despite the presence of reducing borohydride ligands. Similarly, reactions of the same metal halides with four equivalents of Li(CyBH 3 )(Et 2 O) n yielded Th(CyBH 3 ) 4 , U(CyBH 3 ) 4 (thf) 2 , and [Li(Et 2 O) 3 ][Nd(CyBH 3 ) 4 ]. Single crystal X-ray diffraction studies of the M(BnBH 3 ) 4 (thf) 2 complexes with M = Th and U confirmed their formulations. Furthermore, the complexes have approximate D 2d point group symmetry and adopt bicapped hexagonal antiprismatic coordination geometries with axial thf ligands and κ 3 -BnBH 3 ligands bound in the equatorial plane. K[Nd(BnBH 3 ) 4 ] and [Li(Et 2 O) 3 ][Nd(CyBH 3 ) 4 ], which were prepared for comparison to U(III) complexes that were unsuccessfully targeted, were also structurally characterized to reveal complex anions with tetrahedral arrangements of trihydroborate ligands bound to Nd(III). Crystals obtained for Th(CyBH 3 ) 4 and U(CyBH 3 ) 4 (thf) 2 were not suitable for XRD studies, but 1 H and 11 B NMR spectra were consistent with their formulations. Collectively, these complexes represent rare examples of structurally characterized f-element trihydroborate complexes with carbon substituents other than methyl.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Magnetically coupled emission regulator

Magnetic coupling between input and power handling circuits isolates high voltage. A feedback regulator samples the ion source bias current and provides deviation signals to a magnetic amplifier pulse modulator. The pulse modulator controls the dc to ac power inverter which in turn, controls the emission current.

Source record↗

The Bristol method of satellite-improved rainfall monitoring

Remote sensing estimates of area average precipitation are useful to agricultural and climatological applications. Estimates obtained by active or passive microwaves, infrared and visible sensors may be augmented and improved using indirect measures of precipitation, such as the change in near surface soil moisture content caused by a particular event. Measurements of soil moisture using infrared radiances do not provide precipitation information in real time since the sky must clear. However, the resultant estimate of precipitation is a time integrated value which provides a significant savings in data handling and can overcome virtually all of the sampling problems associated with the monitoring of precipitation through storms of long duration.

Barrett, E. C.↗

Probabilistic finite elements

In the Probabilistic Finite Element Method (PFEM), finite element methods have been efficiently combined with second-order perturbation techniques to provide an effective method for informing the designer of the range of response which is likely in a given problem. The designer must provide as input the statistical character of the input variables, such as yield strength, load magnitude, and Young's modulus, by specifying their mean values and their variances. The output then consists of the mean response and the variance in the response. Thus the designer is given a much broader picture of the predicted performance than with simply a single response curve. These methods are applicable to a wide class of problems, provided that the scale of randomness is not too large and the probabilistic density functions possess decaying tails. By incorporating the computational techniques we have developed in the past 3 years for efficiency, the probabilistic finite element methods are capable of handling large systems with many sources of uncertainties. Sample results for an elastic-plastic ten-bar structure and an elastic-plastic plane continuum with a circular hole subject to cyclic loadings with the yield stress on the random field are given.

Belytschko, Ted↗

An efficient software implementation of a variable rate modem

This paper describes the software implementation of the baseband portion of a variable rate modem. The modem can handle arbitrary symbol rates with a fixed input/output sample rate. This approach reduces hardware complexity related to external clock generation circuitry, offers complete flexibility in the selection of symbol rates, and conveniently accommodates symbol timing and symbol rate corrections.

Mantha, Ramesh↗

The Effect of Salts on Electrospray Ionization of Amino Acids in the Negative Mode

The continued search for organics on Mars will require the development of simplified procedures for handling and processing of soil or rock core samples prior to analysis by onboard instrumentation. Extraction of certain organic molecules such as amino acids from rock and soil samples using a liquid solvent (H2O) has been shown to be more efficient (by approximately an order of magnitude) than heat extraction methods. As such, liquid extraction (using H2O) of amino acid molecules from rock cores or regolith material is a prime candidate for the required processing. In this scenario, electrospray ionization (ESI) of the liquid extract would be a natural choice for ionization of the analyte prior to interrogation by one of a variety of potential analytical separation techniques (mass spectroscopy, ion mobility spectroscopy, etc.). Aside from the obvious compatibility of ESI and liquid samples, ESI offers simplicity and a soft ionization capability. In order to demonstrate that liquid extraction and ESI can work as part of an in situ instrument on Mars, we must better understand and quantify the effect salts have on the ESI process. In the current work, we have endeavored to investigate the feasibility and limitations of negative mode ESI of Martian surface samples in the context of sample salt content using ion mobility spectroscopy (IMS).

H I Kim↗

Automated Fluidics Device for Extraction and Quantification of miRNA Biomarkers From Blood

Radiation Assessment DuRing Exposure And long-Duration Spaceflight (RADREADS) demonstrates space-compatible point-of-care technology for quantitative biological monitoring of blood miRNA biomarkers in response to long-term low dose radiation exposure. This individualized monitoring approach will inform targeted treatment strategies to maximize medical resource utilization by accounting for individual susceptibility to radiation-related illnesses. As human spaceflight progresses beyond Earth’s magnetic shielding, radiation exposure poses a significant risk to astronaut health and safety. Extended operation in this environment comes with an increased risk of radiation exposure, leading to higher risks of radiation sickness, cancer, central nervous system effects, and degenerative diseases. While conventional physical dosimetry techniques capture radiation dose, individualistic susceptibility to radiation damage is varied. Multiple characteristics, including age, body weight, sex, genetics, and immune status, have been found to influence radiosensitivity (Liu et al. 2011, and Bouffler 2016). This differential response necessitates individualized monitoring and targeted treatment strategies to maximize medical resource utilization; however, a practical diagnostic platform for quantifying long-term, low dose radiation-induced tissue damage does not currently exist. MicroRNAs (miRNAs) are a class of small, non-coding RNAs that regulate gene expression by mediating the degradation of messenger RNA. The levels of particular miRNAs are influenced by biological processes such as inflammation and serve as biomarkers for a variety of conditions including cancer (Singh et al. 2017). MicroRNAs are found in various bodily fluids and are amenable to collection via liquid biopsies, providing a minimally invasive and easily quantifiable readout for a variety of radiosensitive reporters. A preliminary signature of 15 spaceflight sensitive miRNA has been identified in rodent and human studies, including miR-21-5p, miR-24-3p, miR-92a-3p, miR-17-5p, miR-16a-3p, miR-34a-3p, and miR-223-3p. These targets generally increased expression with radiation dose and linear energy transfer, though variation between individuals is not yet described. Current gaps in the field include a lack of understanding of longitudinal biological responses to long-term, low dose radiation exposure and the absence of space-compatible point-of-care technology for quantitative biological monitoring. In this body of work, we aim to develop an automated bleed-to-read system to process whole blood for the detection of miRNA biomarkers in order to monitor individualistic responses to radiation exposure. This will be achieved via separating serum (or plasma) from whole blood, followed by extraction, amplification, and quantification of the miRNA using a RT-qPCR reaction. Previously, the WetLab-2 hardware enabled execution of a RT-qPCR reaction aboard ISS; however, it is a manual system that requires crew manipulation and bulky components (Parra et al. 2017). To address these issues, automated fluid handling hardware was developed for each stage of sample preparation. Extraction of total RNA is achieved by sequentially pumping reagents through an off-the-shelf nucleic acid binding column (miRNeasy Serum/Plasma Advanced Kit, Qiagen). This approach eliminates several manual pipetting and centrifuging steps and limits the use of toxic chemicals commonly found in other sample processing techniques. The resulting elution will then be automatically dispensed for RT-qPCR analysis using a compact rotary qPCR (Mic qPCR Cycler, Bio Molecular Systems) that will improve spaceflight compatibility by removing bubbles from the detection region, another challenge highlighted by WetLab-2 (Parra et al. 2017). Efforts are also being made to simplify the RT-qPCR reaction to a 1-step air-dryable mix to improve long-term reagent stability at room temperature and reduce system complexity. By automating the RT-qPCR processes via microfluidic manipulation, RADREADS will reduce crewmember hands-on time and enable the personalized detection of radiation-induced tissue damage during long duration missions. Minimally invasive, longitudinal monitoring of individual’s response to radiation exposure will inform how the physiological system responds to long-term low dose space radiation and enables development of targeted countermeasures by the medical team. Ultimately, this portable technology will require minimal technical expertise and can also be used to monitor miRNA biomarkers associated with other diseases.

Tristen Head↗

Center for Isotope Cosmochemistry and Geochronology at NASA Johnson Space Center

The Center for Isotope Cosmochemistry and Geochronology (CICG) at the NASA Johnson Space Center, led by Justin Simon, applies novel elemental and isotopic analytical techniques to understand solar system formation, from processes occurring during the earliest Solar Nebula, to the evolution of planetary bodies during planet formation and differentiation. CICG consists of an integrated suite of labs including dedicated spaces for specialized handling and preparation of meteorites and planetary return samples, metal-free clean chemistry, and mass spectrometry. In addition to a Thermo-Scientific Triton thermal ionization mass spectrometer (TIMS) for high precision isotopic analyses in processed samples, CICG houses two additional mass spectrometry instruments with added laser ablation capabilities for high spatial resolution in-situ measurements: (1) a Thermo-Scientific Element-XR inductively coupled mass spectrometer (ICP-MS) with a Teledyne Photon Machines Analyte Excite+ laser ablation system, and (2) a Nu Sapphire 1700 multi-collector ICP-MS, a large geometry instrument with a multi-pole collision cell for interference removal, with an Applied Spectra J200 tandem laser induced breakdown spectroscopy (LIBS) femto-second laser ablation system. We detail the analytical capabilities of CICG in the context of current and future research projects related to the studies of protoplanetary disk evolution via early-formed Solar System solids, volatile abundances and distribution within the inner solar system, and geochemical and temporal investigations related to planet formation and differentiation. We also highlight opportunities through the relationship with the Center of the Advancement of Space Safety and Mission Assurance Research (CASSMAR) at the University of Texas at El Paso. CICG is open to collaborations and participates in the NASA Facility for Astromaterials Research (NFAR) program, which accepts research proposals for access to the unique facility capabilities.

Jacob B. Setera↗

Computer Controlled High Vacuum Gas Purification and Analysis Line

Light stable isotope work requires the handling of gasses such a way that does not alter isotopic composition. To do this, there are a large number of analytical and experimental procedures which involve the use of a vacuum line, numerous “egg timers” and a human hand on a valve. Unfortunately, the human hand is inconsistent and inadvertent small, and commonly large, differences in timing can have a measurable effect on outcomes. We have constructed a computer controlled high-vacuum line to be used as an expandable platform for future experimental and analytical procedures. The vacuum line consists of an electropolished 316 stainless steel system of cryogenic u-traps partitioned by pneumatic valves. The code to operate the line has been developed using the LabView platform and will allow for automated timing, consistent valve opening speed and unattended operation of long analytical procedures. The aim of this project is to address a need in the light stable isotope laboratory for a general-purpose vacuum line for handling and manipulation of gasses. When combined with existing instrumentation it allows for a significant expansion of current analytical capabilities. The system allows for better handling of standards, gas conversion techniques and gas sample collection for interlaboratory comparisons. The basic structure of the line, automation hardware and software were chosen and designed to provide a base for future expansion of the system to incorporate new automated analytical techniques as laboratory instrumentation and analytical needs expand.

High vacuum↗

Prototype development and test results of a continuous ambient air monitoring system for hydrazine at the 10 ppb level

A Hydrazine Vapor Area Monitor (HVAM) system is currently being field tested as a detector for the presence of hydrazine in ambient air. The MDA/Polymetron Hydrazine Analyzer has been incorporated within the HVAM system as the core detector. This analyzer is a three-electrode liquid analyzer typically used in boiler feed water applications. The HVAM system incorporates a dual-phase sample collection/transport method which simultaneously pulls ambient air samples containing hydrazine and a very dilute sulfuric acid solution (0.0001 M) down a length of 1/4 inch outside diameter (OD) tubing from a remote site to the analyzer. The hydrazine-laden dilute acid stream is separated from the air and the pH is adjusted by addition of a dilute caustic solution to a pH greater than 10.2 prior to analysis. Both the dilute acid and caustic used by the HVAM are continuously generated during system operation on an "as needed" basis by mixing a metered amount of concentrated acid/base with dilution water. All of the waste water generated by the analyzer is purified for reuse by Barnstead ion-exchange cartridges so that the entire system minimizes the generation of waste materials. The pumping of all liquid streams and mixing of the caustic solution and dilution water with the incoming sample are done by a single pump motor fitted with the appropriate mix of peristaltic pump heads. The signal to noise (S/N) ratio of the analyzer has been enhanced by adding a stirrer in the MDA liquid cell to provide mixing normally generated by the high liquid flow rate designed by the manufacturer. An onboard microprocessor continuously monitors liquid levels, sample vacuum, and liquid leak sensors, as well as handles communications and other system functions (such as shut down should system malfunctions or errors occur). The overall system response of the HVAM can be automatically checked at regular intervals by measuring the analyzer response to a metered amount of calibration standard injected into the dilute acid stream. The HVAM system provides two measurement ranges (threshold limit value (TLV): 10 to 1000 parts per billion (ppb)/LEAK: 100 ppb to 10 parts per million (ppm)). The LEAK range is created by dilution of the sulfuric acid/hydrazine liquid sample with pure water. This dual range capability permits the analyzer to quantify ambient air samples whose hydrazine concentrations range from 10 ppb to as high as 10 ppm. The laboratory and field prototypes have demonstrated total system response times on the order of 10 to 12 minutes for samples ranging from 10 to 900 ppb in the lLV mode and is greater than 2 minutes for samples ranging from 100 to 1300 ppb in the LEAK mode. Service intervals of over 3 months have been demonstrated for continuous 24 hour/day, 7 day/week usage. The HVAM is made up of a purged cabinet that contains power supplies, RS422 signal transmission capabilities, a UPS, an on-site warning system, and a Line Replaceable Unit (LRU). The LRU includes all of the liquid flow system, the analyzer, the control/data system microprocessor and assorted flow and liquid-level sensors. The LRU is mounted on a track slide system so it can be serviced inplace or totally removed and quickly exchanged with another calibrated unit, thus minimizing analyzer downtime. Once an LRU is removed from an analyzer enclosure, it can be brought to a laboratory facility for complete calibration and periodic maintenance.

Meneghelli, Barry↗